Previous literature has identified that overall trends in phenology are thought to be shared across the phylogeny for plants (i.e. evolutionary history will influence flowering). We can both: 1) Test this hypothesis in my datasets. 2) Evaluate the overall scope of the tree that we are capturing in this analysis.
Load in Packages
library(rotl) # calls the open tree api to give us a rough idea of the current phylogeny, I would still take these with a grain of salt but its not a bad exploratory option
library(data.table)
library(ggplot2)
library(stringr)
library(tidyverse)
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## ✔ forcats 1.0.0 ✔ tibble 3.2.1
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## ✔ purrr 1.0.2
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
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## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(phytools)
## Loading required package: ape
##
## Attaching package: 'ape'
##
## The following object is masked from 'package:dplyr':
##
## where
##
## Loading required package: maps
##
## Attaching package: 'maps'
##
## The following object is masked from 'package:purrr':
##
## map
library(ape)
Load Data
Simplify to just names and create a simple subset for illustration purposes
Grab a tree for these tips
In order to address both (1) and (2), it may be helpful to label the phylogeny as a overall visual.
Create some labeled plots
New plan, new plan: Find representative taxa 1) That have the best amount of temporal coverage for year by year phenometric measurements
named_data_labeled <- fread("/home/jt-miller/Gurlab/sliding-phenology/data/processed/blooming-period-dataset.csv")
#
flowering_data <- named_data_labeled
result_table <- flowering_data %>%
group_by(speciesName, year) %>%
summarise(
condition_satisfied = n() > 5 & n_distinct(doy) >= 3
) %>%
group_by(speciesName) %>%
summarise(
num_years_condition_satisfied = sum(condition_satisfied)
)
## `summarise()` has grouped output by 'speciesName'. You can override using the
## `.groups` argument.
flowering_data2 <- merge(flowering_data, result_table, by = "speciesName")
flowering_data3 <- flowering_data2 %>%
filter(!bloom_period == "unknown") %>% # doesnt contribute to known phenology
group_by(speciesName) %>%
mutate(bloomSpecificity = case_when(
n_distinct(bloom_period) == 1 & bloom_period == 'spring bloomer' ~ "spring bloomer",
n_distinct(bloom_period) == 1 & bloom_period == 'fall bloomer' ~ "fall bloomer",
n_distinct(bloom_period) > 1 ~ "opportunistic bloomer"
)) %>%
distinct(speciesName, bloomSpecificity, .keep_all = TRUE)
flowering_data4 <- flowering_data3 %>%
filter(num_years_condition_satisfied >= 25)
name_subset <- flowering_data3$speciesName
resolved_subset <- tnrs_match_names(name_subset)
## Warning: , Acmispon rigidus, Malacothamnus enigmaticus, Ottleya strigosa,
## Simpsonanthus jonesii are not matched
# resolved_subset2 <- filter(resolved_subset, !ott_id == 5502771)
# resolved_subset2 <- filter(resolved_subset2, !ott_id == 173589)
# tree_object <- tol_induced_subtree(ott_ids = ott_id(resolved_subset2)) # appends lineages from open tree
in_tree <- is_in_tree(ott_id(resolved_subset))
in_tree
## Abronia villosa Senegalia greggii
## TRUE TRUE
## Acalypha californica Acamptopappus sphaerocephalus
## TRUE TRUE
## Achyronychia cooperi Acmispon americanus
## TRUE TRUE
## Acmispon argophyllus Acmispon glaber
## TRUE TRUE
## Acmispon heermannii Lotus salsuginosus
## TRUE TRUE
## Acmispon micranthus Acmispon strigosus
## TRUE TRUE
## Adenophyllum porophylloides Agave deserti
## TRUE TRUE
## Aliciella latifolia Allionia incarnata
## TRUE TRUE
## Allium fimbriatum Allium monticola
## TRUE TRUE
## Allium peninsulare Amaranthus fimbriatus
## TRUE TRUE
## Ambrosia acanthicarpa Ambrosia dumosa
## TRUE TRUE
## Ambrosia salsola Amsinckia intermedia
## TRUE TRUE
## Amsinckia menziesii Amsinckia tessellata
## TRUE TRUE
## Antirrhinum filipes Aphyllon cooperi
## TRUE TRUE
## Arctostaphylos glauca Argemone munita
## TRUE TRUE
## Aristida adscensionis Aristida purpurea
## TRUE TRUE
## Artemisia ludoviciana Asclepias albicans
## TRUE TRUE
## Asclepias subulata Astragalus aridus
## TRUE TRUE
## Astragalus coccineus Astragalus crotalariae
## TRUE TRUE
## Astragalus didymocarpus Astragalus douglasii
## TRUE TRUE
## Astragalus lentiginosus Astragalus nuttallianus
## TRUE TRUE
## Astragalus palmeri Astragalus tricarinatus
## TRUE TRUE
## Atrichoseris platyphylla Atriplex canescens
## TRUE TRUE
## Atriplex hymenelytra Atriplex polycarpa
## TRUE TRUE
## Ayenia compacta Baccharis brachyphylla
## TRUE TRUE
## Baccharis salicifolia Bahiopsis parishii
## TRUE TRUE
## Baileya multiradiata Baileya pauciradiata
## TRUE TRUE
## Bebbia juncea Bernardia incana
## TRUE TRUE
## Boechera johnstonii Boerhavia coccinea
## TRUE TRUE
## Boerhavia coulteri Boerhavia triquetra
## TRUE TRUE
## Boerhavia wrightii Bouteloua aristidoides
## TRUE TRUE
## Bouteloua barbata Echinopepon bigelovii
## TRUE TRUE
## Brassica tournefortii Brickellia atractyloides
## TRUE TRUE
## Brickellia frutescens Bromus berteroanus
## TRUE TRUE
## Bromus madritensis Bromus tectorum
## TRUE TRUE
## Hoffmannseggia microphylla Cistanthe ambigua
## TRUE TRUE
## Calandrinia ciliata var. menziesii Calochortus concolor
## TRUE TRUE
## Calochortus dunnii Calochortus palmeri
## TRUE TRUE
## Calycoseris parryi Calycoseris wrightii
## TRUE TRUE
## Calyptridium monandrum Camissonia brevipes
## TRUE FALSE
## Eulobus californicus Camissonia cardiophylla
## TRUE FALSE
## Chylismia claviformis Camissonia pallida
## TRUE FALSE
## Eremothera refracta Camissoniopsis bistorta
## TRUE TRUE
## Camissoniopsis confusa Camissoniopsis pallida
## TRUE TRUE
## Castilleja exserta Castilleja foliolosa
## TRUE TRUE
## Castilleja minor Streptanthus cooperi
## TRUE TRUE
## Caulanthus hallii Caulanthus lasiophyllus
## TRUE TRUE
## Caulanthus simulans Ceanothus perplexans
## TRUE FALSE
## Cenchrus setaceus Centaurea melitensis
## TRUE TRUE
## Cercocarpus betuloides Chaenactis artemisiifolia
## TRUE TRUE
## Chaenactis carphoclinia Chaenactis fremontii
## TRUE TRUE
## Chaenactis glabriuscula Chaenactis stevioides
## TRUE TRUE
## Euphorbia polycarpa Chenopodiastrum murale
## TRUE TRUE
## Chenopodiastrum murale Chilopsis linearis
## TRUE TRUE
## Chorizanthe brevicornu Chorizanthe corrugata
## TRUE TRUE
## Chorizanthe fimbriata Chorizanthe rigida
## TRUE TRUE
## Chylismia brevipes Chylismia cardiophylla
## TRUE TRUE
## Chylismia claviformis Cistanthe ambigua
## TRUE TRUE
## Claytonia parviflora Cleomella arborea
## TRUE TRUE
## Cleomella arborea Cleomella obtusifolia
## TRUE TRUE
## Coleogyne ramosissima Condea emoryi
## TRUE TRUE
## Corethrogyne filaginifolia Crassula connata
## TRUE TRUE
## Crossosoma bigelovii Croton californicus
## TRUE TRUE
## Johnstonella angustifolia Cryptantha barbigera
## TRUE TRUE
## Johnstonella holoptera Cryptantha decipiens
## TRUE TRUE
## Cryptantha ganderi Cryptantha intermedia
## TRUE TRUE
## Cryptantha maritima Eremocarya micrantha
## TRUE TRUE
## Cryptantha muricata Cryptantha nevadensis
## TRUE TRUE
## Cryptantha pterocarya Cryptantha racemosa
## TRUE TRUE
## Cryptantha utahensis Cucurbita palmata
## TRUE TRUE
## Cuscuta californica Cuscuta psorothamnensis
## TRUE TRUE
## Cylindropuntia bigelovii Cylindropuntia echinocarpa
## TRUE TRUE
## Cylindropuntia fosbergii Cylindropuntia ganderi
## TRUE TRUE
## Cylindropuntia ramosissima Dalea mollis
## TRUE TRUE
## Dalea mollissima Datura discolor
## TRUE TRUE
## Datura wrightii Delphinium parishii
## TRUE TRUE
## Dendromecon rigida Descurainia pinnata
## TRUE TRUE
## Dicoria canescens Dimorphotheca sinuata
## TRUE TRUE
## Diplacus bigelovii Diplacus calycinus
## TRUE TRUE
## Dichelostemma capitatum Ditaxis lanceolata
## TRUE TRUE
## Ditaxis serrata Ditaxis serrata
## TRUE TRUE
## Dithyrea californica Tomostima cuneifolia
## TRUE TRUE
## Dudleya pulverulenta Dudleya lanceolata
## TRUE TRUE
## Dudleya saxosa Echinocereus engelmannii
## TRUE TRUE
## Ehrendorferia chrysantha Emmenanthe penduliflora
## TRUE TRUE
## Encelia actoni Encelia farinosa
## TRUE FALSE
## Encelia frutescens Ephedra aspera
## TRUE TRUE
## Epilobium canum Epipactis gigantea
## TRUE TRUE
## Eremalche exilis Eremalche rotundifolia
## TRUE TRUE
## Eremocarya lepida Eremocarya micrantha
## TRUE TRUE
## Eremothera boothii Eremothera chamaenerioides
## TRUE TRUE
## Eremothera refracta Eriastrum densifolium
## TRUE TRUE
## Eriastrum diffusum Eriastrum eremicum
## TRUE TRUE
## Ericameria brachylepis Ericameria linearifolia
## TRUE TRUE
## Ericameria paniculata Conyza bonariensis
## TRUE TRUE
## Erigeron canadensis Eriodictyon crassifolium
## TRUE TRUE
## Eriodictyon trichocalyx Eriogonum deflexum
## TRUE TRUE
## Eriogonum elongatum Eriogonum fasciculatum
## TRUE TRUE
## Eriogonum gracile Eriogonum inflatum
## TRUE TRUE
## Eriogonum pusillum Eriogonum reniforme
## TRUE TRUE
## Eriogonum thomasii Eriogonum thurberi
## TRUE TRUE
## Eriogonum trichopes Eriogonum wrightii
## TRUE TRUE
## Eriophyllum ambiguum Eriophyllum confertiflorum
## TRUE TRUE
## Eriophyllum wallacei Erodium cicutarium
## TRUE TRUE
## Erodium texanum Erythranthe cardinalis
## TRUE TRUE
## Erythranthe floribunda Erythranthe guttata
## TRUE TRUE
## Erythranthe parishii Eschscholzia androuxii
## TRUE TRUE
## Eschscholzia californica Eschscholzia minutiflora
## TRUE TRUE
## Eschscholzia papastillii Eschscholzia parishii
## TRUE TRUE
## Eucrypta chrysanthemifolia Eucrypta micrantha
## TRUE TRUE
## Eulobus californicus Euphorbia abramsiana
## TRUE TRUE
## Euphorbia arizonica Euphorbia eriantha
## TRUE TRUE
## Euphorbia melanadenia Euphorbia micromera
## TRUE TRUE
## Euphorbia pediculifera Euphorbia polycarpa
## TRUE TRUE
## Euphorbia setiloba Eustoma exaltatum
## TRUE TRUE
## Fagonia laevis Fagonia pachyacantha
## TRUE TRUE
## Ferocactus cylindraceus Festuca bromoides
## TRUE TRUE
## Festuca octoflora Fouquieria splendens
## TRUE TRUE
## Funastrum cynanchoides Funastrum cynanchoides
## TRUE TRUE
## Funastrum hirtellum Galium angustifolium
## TRUE TRUE
## Galium stellatum Geraea canescens
## TRUE TRUE
## Gilia angelensis Gilia capitata
## TRUE TRUE
## Gilia scopulorum Gilia stellata
## TRUE TRUE
## Gutierrezia californica Gutierrezia sarothrae
## TRUE TRUE
## Helianthus annuus Helianthus petiolaris
## TRUE TRUE
## Heliotropium curassavicum Hesperocallis undulata
## TRUE TRUE
## Hesperoyucca whipplei Hibiscus denudatus
## TRUE TRUE
## Hilaria rigida Hirschfeldia incana
## TRUE TRUE
## Hoffmannseggia microphylla Hordeum murinum
## TRUE TRUE
## Horsfordia newberryi Hulsea vestita
## TRUE TRUE
## Ambrosia salsola Condea emoryi
## TRUE TRUE
## Isocoma acradenia Cleomella arborea
## TRUE TRUE
## Johnstonella angustifolia Johnstonella costata
## TRUE TRUE
## Cryptantha racemosa Juncus bufonius
## TRUE TRUE
## Justicia californica Kallstroemia californica
## TRUE TRUE
## Keckiella antirrhinoides Krameria bicolor
## TRUE TRUE
## Krameria erecta Krameria grayi
## TRUE TRUE
## Langloisia setosissima Larrea tridentata
## TRUE TRUE
## Lasthenia coronaria Lasthenia gracilis
## TRUE TRUE
## Layia glandulosa Lepidium fremontii
## TRUE TRUE
## Lepidium lasiocarpum Lepidospartum squamatum
## TRUE TRUE
## Leptosiphon chrysanthus Leptosiphon lemmonii
## TRUE TRUE
## Leptosyne bigelovii Leptosyne californica
## TRUE TRUE
## Lilium parryi Linanthus dianthiflorus
## TRUE TRUE
## Linanthus jonesii Linanthus maculatus
## TRUE TRUE
## Loeflingia squarrosa Langloisia matthewsii
## TRUE TRUE
## Loeseliastrum schottii Filago arizonica
## TRUE TRUE
## Filago depressa Filago californica
## TRUE TRUE
## Lotus scoparius Lotus strigosus
## TRUE TRUE
## Bromus tomentellus Lupinus arizonicus
## TRUE TRUE
## Lupinus bicolor Lupinus concinnus
## TRUE TRUE
## Lupinus hirsutissimus Lupinus shockleyi
## TRUE TRUE
## Lupinus sparsiflorus Lupinus truncatus
## TRUE TRUE
## Lycium andersonii Lycium brevipes
## TRUE TRUE
## Lycium cooperi Lycium fremontii
## TRUE TRUE
## Lyrocarpa coulteri Lythrum californicum
## TRUE TRUE
## Malacothamnus fasciculatus Malacothrix glabrata
## TRUE TRUE
## Malacothrix stebbinsii Malva parviflora
## TRUE TRUE
## Mammillaria dioica Marah macrocarpa
## TRUE TRUE
## Marina parryi Medicago lupulina
## TRUE TRUE
## Medicago polymorpha Melica frutescens
## TRUE TRUE
## Melica imperfecta Melilotus albus
## TRUE TRUE
## Melilotus indicus Mentzelia affinis
## TRUE TRUE
## Mentzelia albicaulis Mentzelia desertorum
## TRUE TRUE
## Mentzelia hirsutissima Mentzelia involucrata
## TRUE TRUE
## Mentzelia jonesii Mesembryanthemum nodiflorum
## TRUE TRUE
## Mimetanthe pilosa Diplacus bigelovii
## TRUE TRUE
## Mirabilis laevis Mirabilis multiflora
## TRUE TRUE
## Mirabilis tenuiloba Mohavea confertiflora
## TRUE TRUE
## Monoptilon bellioides Muhlenbergia microsperma
## TRUE TRUE
## Muilla maritima Nama demissa
## TRUE TRUE
## Nama hispida Nasturtium officinale
## TRUE TRUE
## Prosopis glandulosa Spiranthes odorata
## TRUE TRUE
## Nemacladus glanduliferus Nemacladus orientalis
## TRUE TRUE
## Nemacladus rubescens Nemacladus tenuis
## TRUE TRUE
## Nemophila menziesii Neogaerrhinum filipes
## TRUE TRUE
## Nicotiana attenuata Nicotiana clevelandii
## TRUE TRUE
## Nicotiana glauca Nicotiana obtusifolia
## TRUE TRUE
## Nicotiana quadrivalvis Nolina bigelovii
## TRUE TRUE
## Nolina parryi Oenothera deltoides
## TRUE TRUE
## Oenothera elata Oligomeris linifolia
## TRUE TRUE
## Olneya tesota Oncosiphon piluliferus
## TRUE TRUE
## Oncosiphon piluliferus Opuntia basilaris
## TRUE TRUE
## Opuntia phaeacantha Aphyllon cooperi
## TRUE TRUE
## Palafoxia arida Pappostipa speciosa
## TRUE TRUE
## Parietaria hespera Parkinsonia aculeata
## TRUE TRUE
## Parkinsonia florida Pectis papposa
## TRUE TRUE
## Pectocarya anisocarpa Pectocarya heterocarpa
## TRUE TRUE
## Pectocarya linearis Pectocarya peninsularis
## TRUE TRUE
## Pectocarya platycarpa Pectocarya recurvata
## TRUE TRUE
## Pectocarya setosa Cenchrus setaceus
## TRUE TRUE
## Penstemon californicus Penstemon centranthifolius
## TRUE TRUE
## Penstemon clevelandii Cleomella arborea
## TRUE TRUE
## Perityle emoryi Petalonyx thurberi
## TRUE TRUE
## Peucephyllum schottii Phacelia crenulata
## TRUE TRUE
## Phacelia brachyloba Phacelia campanularia
## TRUE TRUE
## Phacelia cicutaria Phacelia crenulata
## TRUE TRUE
## Phacelia cryptantha Phacelia distans
## TRUE TRUE
## Phacelia ivesiana Phacelia minor
## TRUE TRUE
## Phacelia neglecta Phacelia pedicellata
## TRUE TRUE
## Phacelia ramosissima Phacelia rotundifolia
## TRUE TRUE
## Phalaris minor Pholisma arenarium
## TRUE TRUE
## Pholistoma membranaceum Phoradendron californicum
## TRUE TRUE
## Physalis crassifolia Physaria tenella
## TRUE TRUE
## Pilostyles thurberi Plagiobothrys arizonicus
## TRUE TRUE
## Plantago ovata Plantago patagonica
## TRUE TRUE
## Hilaria rigida Pleurocoronis pluriseta
## TRUE TRUE
## Pluchea sericea Poa secunda
## TRUE TRUE
## Polypogon monspeliensis Porophyllum gracile
## TRUE TRUE
## Proboscidea altheifolia Prosopis glandulosa
## TRUE TRUE
## Prunus fasciculata Prunus fremontii
## TRUE TRUE
## Psathyrotes ramosissima Pseudognaphalium biolettii
## TRUE TRUE
## Pseudoziziphus parryi Psorothamnus arborescens
## TRUE TRUE
## Psorothamnus emoryi Psorothamnus schottii
## TRUE TRUE
## Psorothamnus spinosus Pterostegia drymarioides
## TRUE TRUE
## Pulicaria paludosa Rafinesquia californica
## TRUE TRUE
## Rafinesquia neomexicana Rhus aromatica
## TRUE TRUE
## Rhus ovata Ribes indecorum
## TRUE TRUE
## Salix exigua Salix gooddingii
## TRUE TRUE
## Salix laevigata Salsola paulsenii
## TRUE TRUE
## Salsola tragus Saltugilia australis
## TRUE TRUE
## Saltugilia latimeri Salvia apiana
## TRUE TRUE
## Salvia carduacea Salvia columbariae
## FALSE TRUE
## Salvia eremostachya Salvia greatae
## TRUE TRUE
## Salvia vaseyi Sambucus nigra subsp. caerulea
## FALSE TRUE
## Funastrum cynanchoides Schismus arabicus
## TRUE TRUE
## Schismus barbatus Scrophularia californica
## TRUE TRUE
## Scutellaria mexicana Senecio californicus
## TRUE TRUE
## Senecio mohavensis Senegalia greggii
## TRUE TRUE
## Senna armata Senna artemisioides
## TRUE TRUE
## Senna covesii Sesuvium verrucosum
## TRUE TRUE
## Sidotheca emarginata Simmondsia chinensis
## TRUE TRUE
## Sisymbrium irio Sisymbrium orientale
## TRUE TRUE
## Solanum douglasii Solanum parishii
## TRUE TRUE
## Solanum umbelliferum Solidago velutina
## TRUE TRUE
## Sonchus asper Sonchus oleraceus
## TRUE TRUE
## Sphaeralcea ambigua Stanleya pinnata
## TRUE TRUE
## Stemodia durantifolia Stephanomeria exigua
## TRUE TRUE
## Stephanomeria pauciflora Stillingia linearifolia
## TRUE TRUE
## Stillingia spinulosa Stipa capensis
## TRUE TRUE
## Stipa hymenoides Pappostipa speciosa
## TRUE TRUE
## Streptanthella longirostris Streptanthella longirostris
## TRUE TRUE
## Stylocline gnaphaloides Tamarix aphylla
## TRUE TRUE
## Tamarix ramosissima Tetracoccus fasciculatus
## TRUE TRUE
## Thamnosma montana Caulanthus lasiophyllus
## TRUE TRUE
## Thymophylla pentachaeta Thysanocarpus curvipes
## TRUE TRUE
## Tidestromia oblongifolia Tidestromia suffruticosa
## FALSE TRUE
## Tiquilia canescens Tiquilia palmeri
## TRUE TRUE
## Tiquilia plicata Tomostima cuneifolia
## TRUE TRUE
## Trianthema portulacastrum Tribulus terrestris
## TRUE TRUE
## Trichoptilium incisum Trixis californica
## TRUE TRUE
## Tropidocarpum gracile Uropappus lindleyi
## TRUE TRUE
## Veronica anagallis-aquatica Volutaria tubuliflora
## TRUE TRUE
## Xylorhiza cognata Xylorhiza orcuttii
## TRUE TRUE
## Xylorhiza tortifolia Yucca schidigera
## TRUE TRUE
## Zeltnera venusta Pseudoziziphus parryi
## TRUE TRUE
tr <- tol_induced_subtree(ott_id(resolved_subset)[in_tree])
##
Progress [--------------------------------] 0/1935 ( 0%) ?s
Progress [============================] 1935/1935 (100%) 0s
## Warning in collapse_singles(tr, show_progress): Dropping singleton nodes with
## labels: Magnoliopsida ott99252, mrcaott2ott2645, mrcaott2ott35778,
## Mesangiospermae ott5298374, mrcaott2ott10930, mrcaott2ott969, mrcaott2ott62529,
## mrcaott2ott8379, eudicotyledons ott431495, Gunneridae ott853757,
## mrcaott2ott8384, mrcaott2ott1479, mrcaott2ott345, Malpighiales ott429482,
## mrcaott345ott22364, mrcaott345ott18689, mrcaott345ott177705,
## mrcaott345ott38722, mrcaott345ott24237, mrcaott345ott30307, mrcaott345ott26478,
## mrcaott345ott191443, mrcaott345ott485790, Euphorbieae ott520955,
## mrcaott345ott1030065, mrcaott8051ott28703, mrcaott8051ott30309,
## mrcaott33275ott41973, mrcaott33275ott402542, mrcaott33275ott334199,
## mrcaott33275ott33286, Euphorbia sect. Poinsettia ott5147152, Euphorbia subsect.
## Erianthae ott5147154, mrcaott42861ott253647, mrcaott42861ott42866,
## mrcaott42861ott343513, mrcaott42861ott124900, mrcaott376444ott1005185,
## mrcaott42868ott72820, mrcaott716894ott7056399, mrcaott550766ott989270,
## mrcaott30323ott34866, mrcaott504ott36284, mrcaott504ott10167,
## mrcaott10167ott241549, mrcaott10167ott64672, mrcaott10167ott52218,
## mrcaott52218ott764979, mrcaott52218ott262937, Bernardia (genus in kingdom
## Archaeplastida) ott523028, mrcaott30317ott209327, mrcaott30317ott72561,
## mrcaott72561ott147420, mrcaott147420ott610290, mrcaott147420ott230733,
## mrcaott147420ott190669, mrcaott147420ott402227, mrcaott147420ott816389,
## Acalypha ott560972, mrcaott170575ott211956, mrcaott6748ott423256,
## mrcaott6748ott30319, mrcaott6748ott6752, mrcaott6752ott362813,
## mrcaott6752ott174819, mrcaott6752ott671151, mrcaott6752ott6762,
## mrcaott6762ott16262, mrcaott6762ott19547, mrcaott6762ott592498,
## mrcaott6762ott6764, mrcaott6762ott426179, mrcaott6762ott24605,
## mrcaott6762ott16264, mrcaott16264ott16279, mrcaott16264ott426168,
## mrcaott3949ott15752, mrcaott3949ott28711, Picrodendraceae ott62391,
## mrcaott28711ott28714, mrcaott28714ott788306, Tetracoccus (genus in domain
## Eukaryota) ott33336, mrcaott3853ott8858, mrcaott8858ott33097,
## mrcaott8858ott12186, mrcaott8858ott98085, Salicaceae ott530183,
## mrcaott8858ott270454, mrcaott8858ott703490, mrcaott8858ott33085,
## mrcaott8858ott102531, mrcaott8858ott502530, mrcaott8858ott737360,
## mrcaott8858ott474976, Saliceae ott509390, mrcaott86747ott895191,
## mrcaott86747ott531336, mrcaott531336ott725903, mrcaott725903ott738780,
## mrcaott725903ott795555, mrcaott164187ott164212, mrcaott164212ott567279,
## mrcaott567279ott786842, mrcaott567279ott567287, mrcaott567279ott738777,
## mrcaott371ott63303, mrcaott371ott42100, mrcaott371ott22991, Urticaceae
## ott658494, mrcaott22991ott23000, mrcaott22991ott266711, mrcaott22991ott431744,
## mrcaott431744ott723994, mrcaott431744ott472752, Parietaria ott630640,
## mrcaott773ott137975, Rhamnaceae ott329916, Pseudoziziphus ott7056810, Rosaceae
## ott208036, Amygdaloideae ott731134, mrcaott10421ott156934,
## mrcaott156934ott295908, Kerrieae ott901804, mrcaott538527ott817076, Coleogyne
## ott817078, mrcaott34671ott244226, mrcaott61998ott1012886,
## mrcaott61998ott132521, mrcaott61998ott1018655, mrcaott61998ott990519,
## mrcaott61998ott946407, Dryadoideae ott366727, mrcaott122440ott207997,
## mrcaott122440ott653075, mrcaott653075ott7056984, mrcaott2511ott32687,
## mrcaott2511ott253321, mrcaott2511ott29878, Cucurbitaceae ott1006267,
## mrcaott2511ott4028, mrcaott2511ott2972, mrcaott2511ott376422,
## mrcaott2511ott351037, mrcaott2511ott14789, mrcaott2511ott14774,
## mrcaott2511ott182773, mrcaott2511ott185940, mrcaott2511ott132044,
## mrcaott2511ott2520, mrcaott2520ott14778, mrcaott2520ott11772, Cucurbiteae
## ott77740, mrcaott11772ott84409, mrcaott84409ott337509, mrcaott84409ott841310,
## mrcaott84409ott841300, Cucurbita (genus in kingdom Archaeplastida) ott379277,
## Sicyoeae ott462358, mrcaott4000ott103106, mrcaott4000ott67706,
## mrcaott4000ott10298, mrcaott10298ott870455, mrcaott10298ott103086,
## mrcaott103086ott103110, Marah ott1066441, mrcaott198664ott212996, Echinopepon
## ott198658, mrcaott309341ott337493, mrcaott309341ott760212, Apodanthaceae
## ott167651, Pilostyles ott809744, Fabales ott956360, mrcaott579ott179386,
## Fabaceae ott560323, mrcaott579ott730, mrcaott579ott45621, mrcaott579ott8603,
## Papilionoideae ott39538, mrcaott579ott5468, mrcaott579ott5457,
## mrcaott579ott5462, mrcaott579ott5470, mrcaott579ott5091, mrcaott579ott5515,
## mrcaott579ott38037, mrcaott579ott7223, mrcaott579ott11248,
## mrcaott11248ott11254, mrcaott11248ott120275, mrcaott11248ott25572,
## mrcaott11248ott75662, mrcaott11248ott24174, mrcaott11248ott11252,
## mrcaott11248ott192321, mrcaott11248ott24170, mrcaott11248ott11264,
## mrcaott11248ott24172, mrcaott11250ott314143, mrcaott11250ott62867,
## mrcaott11250ott11262, mrcaott11250ott62865, mrcaott11250ott132250,
## mrcaott11250ott11258, mrcaott11258ott752495, mrcaott11258ott532649,
## mrcaott11258ott279712, mrcaott11258ott532657, mrcaott11258ott583880,
## mrcaott363910ott462258, mrcaott462258ott563646, mrcaott462258ott596943,
## mrcaott1749ott496549, mrcaott1749ott222250, mrcaott1749ott27613,
## mrcaott1749ott38031, mrcaott38031ott42707, Medicago ott1086823,
## mrcaott38031ott209352, mrcaott38031ott424990, mrcaott38031ott525750,
## mrcaott38031ott170192, mrcaott38031ott193971, mrcaott38031ott760436,
## mrcaott38031ott193970, mrcaott38032ott646077, mrcaott38032ott374489,
## mrcaott38032ott950610, mrcaott38042ott139477, mrcaott38042ott230316,
## mrcaott38042ott262308, mrcaott38042ott1007989, mrcaott38042ott989938,
## mrcaott38042ott771616, mrcaott368370ott1072867, mrcaott34386ott72192,
## mrcaott34386ott253732, mrcaott34386ott42465, mrcaott42465ott1001097,
## mrcaott449763ott526191, mrcaott449763ott931832, Robinieae ott563850,
## mrcaott37541ott114493, mrcaott37541ott688634, Olneya ott688641,
## mrcaott3942ott82511, dalbergioids sensu lato ott7055847, Amorpheae ott615877,
## mrcaott3942ott763790, mrcaott189642ott334591, Marina ott918581,
## mrcaott189643ott189644, mrcaott189643ott920345, mrcaott240355ott240366,
## mrcaott240366ott1090116, mrcaott240366ott240370, mrcaott341195ott763792,
## mrcaott341195ott763784, mrcaott5473ott26267, mrcaott5473ott590008,
## mrcaott5473ott46797, mrcaott5473ott165471, mrcaott5473ott8026,
## mrcaott8026ott33311, mrcaott8026ott31847, Genisteae ott1090346,
## mrcaott8026ott62394, mrcaott8026ott908606, mrcaott8026ott224618,
## mrcaott8026ott398890, mrcaott8026ott8519, mrcaott8519ott726487, Lupinus
## ott878988, mrcaott8519ott222530, mrcaott8519ott388496, mrcaott8519ott553518,
## mrcaott8519ott857028, mrcaott8519ott222528, mrcaott8519ott282245,
## mrcaott282245ott902823, mrcaott902823ott1065704, mrcaott185311ott539267,
## mrcaott265614ott857024, mrcaott265634ott740409, mrcaott265634ott792139,
## mrcaott265634ott282243, mrcaott282243ott940870, mrcaott2644ott112865,
## mrcaott2644ott30537, mrcaott2644ott86941, mrcaott2644ott333121,
## mrcaott2644ott33732, mrcaott2644ott72925, mrcaott2644ott72932,
## mrcaott72932ott87429, mrcaott87429ott471741, mrcaott87429ott471728,
## mrcaott87429ott471732, Hoffmannseggia ott702632, mrcaott321621ott517678,
## mrcaott321621ott896099, mrcaott896099ott923019, mrcaott21759ott946962,
## mrcaott21759ott170059, mrcaott21759ott124017, Senna ott404633,
## mrcaott21759ott68521, mrcaott21759ott148479, mrcaott21759ott68517,
## mrcaott21759ott148477, mrcaott21759ott147099, mrcaott21759ott326851,
## mrcaott21759ott234461, mrcaott21759ott148490, mrcaott68511ott335063,
## mrcaott68511ott234453, mrcaott234453ott757700, mrcaott757700ott808767,
## mrcaott757700ott757709, mrcaott757700ott908908, mrcaott8605ott87214,
## mrcaott8605ott220379, mrcaott8605ott40823, mrcaott8605ott308458,
## mrcaott8605ott659681, mrcaott8605ott26386, mrcaott8613ott472478,
## mrcaott8613ott66199, mrcaott8613ott66193, mrcaott8613ott981814,
## mrcaott8878ott17129, mrcaott8878ott61940, mrcaott61940ott444652,
## mrcaott444652ott479055, mrcaott39645ott65125, mrcaott39645ott233743,
## mrcaott39645ott471736, mrcaott39645ott39654, mrcaott39654ott39656,
## mrcaott39658ott366575, mrcaott366575ott452957, mrcaott444638ott879743,
## Zygophylloideae ott518751, mrcaott2737ott159002, mrcaott2737ott158973,
## mrcaott2737ott158965, mrcaott2737ott760110, mrcaott2738ott2742, Larreoideae
## ott518759, mrcaott199325ott359651, mrcaott199325ott250015, Larrea ott185819,
## mrcaott250015ott414990, mrcaott87296ott462596, mrcaott87296ott199322,
## Tribuloideae ott518754, mrcaott1091855ott3902318, Krameriaceae ott1074652,
## mrcaott464458ott596333, mrcaott464458ott464459, mrcaott571539ott595139,
## mrcaott595139ott1091
#ape::plot.phylo(tr, cex = 1.5, type = "phylogram") # edges are being a pain...seems the whole tree was pruned...yay
Plotting
ott_ids <- tr[[2]]
ott_ids <- gsub("[^0-9 ]", "", ott_ids)
ott_names <- gsub("\\d+", "", tr[[2]])
ott_names <- gsub("\\_ott", "", ott_names)
ott_names <- gsub("_", " ", ott_names)
tree_df <- data.frame(ott_ids, ott_names)
tree_df <- tree_df %>%
rename(speciesName = ott_names)
result_df <- tree_df %>%
left_join(flowering_data3, by = "speciesName")
trait_df <- result_df
#resolved_subset_m <- merge(resolved_tr_subset, flowering_data3, by.x = "unique_name", by.y = "speciesName")
#trait_df <- merge(tree_df, flowering_data3, by.x = "ott_names", by.y = "speciesName",)
tr # try storing the list into this tree objM
##
## Phylogenetic tree with 473 tips and 360 internal nodes.
##
## Tip labels:
## Euphorbia_eriantha_ott776654, Euphorbia_abramsiana_ott42861, Euphorbia_pediculifera_ott1005185, Euphorbia_arizonica_ott42868, Euphorbia_polycarpa_ott72822, Euphorbia_micromera_ott989270, ...
## Node labels:
## Spermatophyta ott10218, mrcaott2ott121, mrcaott2ott2441, Pentapetalae ott5316182, mrcaott2ott2464, rosids ott1008296, ...
##
## Rooted; no branch lengths.
# Sort the merged dataframe based on the order of ott_names in tree_df
trait_df <- trait_df[order(match(trait_df$speciesName, tree_df$speciesName)), ]
trait_df <- select(result_df, ott_ids, speciesName, bloomSpecificity, num_years_condition_satisfied)
trait_df <- trait_df %>%
mutate(bloomCol = case_when(
is.na(bloomSpecificity) ~ "grey",
bloomSpecificity == "spring bloomer" ~ "darkgreen",
bloomSpecificity == "fall bloomer" ~ "darkred",
bloomSpecificity == "opportunistic bloomer" ~ "goldenrod"
))
#ordered_trait_vector <- trait_df$bloomCol[order(match(trait_df$ott_names, trait_df$ott_names))]
tr$traits <- trait_df$bloomCol
ape::plot.phylo(tr, cex = 1.5, type = "phylogram", tip.color = tr$traits) # edges are being a pain...
How do the phenometrics look?
# trait_df <- trait_df %>%
# mutate(phenometric_scope =
# case_when(
# num_years_condition_satisfied < 10 ~ "grey",
# num_years_condition_satisfied >= 10 & num_years_condition_satisfied < 20 ~ "steelblue",
# num_years_condition_satisfied >= 20~ "purple",
# TRUE ~ "pink"
#
# ))
#
# ape::plot.phylo(tr, cex = 1.5, type = "phylogram", tip.color = trait_df$phenometric_scope) # edges are being a pain...
Some sample data for the package ape